Single cell and population transcriptomics reveal epithelial remodeling in type 2-high asthma

BACKGROUND: The type 2 cytokine-high asthma endotype (T2H) is characterized by IL-13-driven mucus obstruction of the airways. To investigate this poorly understood pathobiology, we characterized IL-13 effects on human airway epithelial cultures using single cell RNA-sequencing, finding that IL-13 generated a novel transcriptional state for each cell type. Specifically, we discovered a mucus secretory program induced by IL-13 in all cell types which converted both mucus and defense secretory cells into a metaplastic state with emergent mucin production and secretion, while leading to ER stress and cell death in ciliated cells. The IL-13-remodeled epithelium secreted a pathologic, mucin-imbalanced, and innate immunity-depleted proteome that arrested mucociliary motion. Signatures of IL-13-induced cellular remodeling were mirrored by transcriptional signatures characteristic of the nasal airway epithelium within T2H versus T2-low asthmatic children. Our results reveal the epithelium-wide scope of T2H asthma and present novel therapeutic targets for restoring normal epithelial function. Overall design: Single cell transcriptomics was carried out for experiments involving either acute (48 hours) or chronic (11 days) stimulation with IL-13 (or mock stimulation with BSA) of air-liquid interface (ALI) cultures grown from epithelial cells taken from two tracheal donors. For the acute stimulation experiment, we sequenced a total of 2,385 cells, plus positive and negative controls (1,894 remaining after QC). For the chronic stimulation experiment, we sequenced a total of 802 single cells (756 remaining after QC and batch correction).